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Updated preprocessing: sample preparation using new PrepareSample class

This MR implements the first version of the new PrepareSamples class, making everything independent of hardcoded flavours.

Furthermore, it removes the merging step. The output h5 files of the sample preparation are now written out incrementally.

Finally, the MR carries over latest changes in the master branch.

related to &1 (closed)

Edited by Philipp Gadow

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